A multi-country phase 2 study to evaluate the suitcase lab for rapid detection of SARS-CoV-2 in seven Sub-Saharan African countries: Lessons from the field

Background : The COVID-19 pandemic led to severe health systems collapse, as well as logistics and supply delivery shortages across sectors. Delivery of PCR related healthcare supplies continue to be hindered. There is the need for a rapid and accessible SARS-CoV-2 molecular detection method in low resource settings. Objectives : To validate a novel isothermal amplification method for rapid detection of SARS-CoV-2 across seven sub-Sharan African countries. Study design : In this multi-country phase 2 diagnostic study, 3,231 clinical samples in seven African sites were tested with two reverse transcription Recombinase-Aided Amplification (RT-RAA) assays (based on SARS-CoV-2 Nucleocapsid (N) gene and RNA-dependent RNA polymerase (RdRP) gene). The test was performed in a mobile suitcase laboratory within 15 minutes. All results were compared to a real-time RT-PCR assay. Extraction kits based on silica gel or magnetic beads were applied. Results : Four sites demonstrated good to excellent agreement, while three sites showed fair to moderate results. The RdRP gene assay exhibited an overall PPV of 0.92 and a NPV of 0.88. The N gene assay exhibited an overall PPV of 0.93 and a NPV 0.88. The sensitivity of both RT-RAA assays varied depending on the sample Ct values. When comparing sensitivity between sites, values differed considerably. For high viral load samples, the RT-RAA assay sensitivity ranges were between 60.5 and 100% (RdRP assay) and 25 and 98.6 (N assay). Conclusion : Overall, the RdRP based RT-RAA test showed the best assay accuracy. This study highlights the challenges of implementing rapid molecular assays in field conditions. Factors that are important for successful deployment across countries include the implementation of standardized operation procedures, in-person continuous training for staff, and enhanced quality control measures.

A multi-country phase 2 study to evaluate the suitcase lab for rapid detection of SARS-CoV-2 in seven Sub-Saharan African countries: Lessons from the field.

BACKGROUND: The COVID-19 pandemic led to severe health systems collapse, as well as logistics and supply delivery shortages across sectors. Delivery of PCR related healthcare supplies continue to be hindered. There is the need for a rapid and accessible SARS-CoV-2 molecular detection method in low resource settings. OBJECTIVES: To validate a novel isothermal amplification method for rapid detection of SARS-CoV-2 across seven sub-Sharan African countries. STUDY DESIGN: In this multi-country phase 2 diagnostic study, 3,231 clinical samples in seven African sites were tested with two reverse transcription Recombinase-Aided Amplification (RT-RAA) assays (based on SARS-CoV-2 Nucleocapsid (N) gene and RNA-dependent RNA polymerase (RdRP) gene). The test was performed in a mobile suitcase laboratory within 15 min. All results were compared to a real-time RT-PCR assay. Extraction kits based on silica gel or magnetic beads were applied. RESULTS: Four sites demonstrated good to excellent agreement, while three sites showed fair to moderate results. The RdRP gene assay exhibited an overall PPV of 0.92 and a NPV of 0.88. The N gene assay exhibited an overall PPV of 0.93 and a NPV 0.88. The sensitivity of both RT-RAA assays varied depending on the sample Ct values. When comparing sensitivity between sites, values differed considerably. For high viral load samples, the RT-RAA assay sensitivity ranges were between 60.5 and 100% (RdRP assay) and 25 and 98.6 (N assay). CONCLUSION: Overall, the RdRP based RT-RAA test showed the best assay accuracy. This study highlights the challenges of implementing rapid molecular assays in field conditions. Factors that are important for successful deployment across countries include the implementation of standardized operation procedures, in-person continuous training for staff, and enhanced quality control measures.

High Severe Acute Respiratory Syndrome Coronavirus 2 Antibody Prevalence After the Third Epidemic Wave (May-October 2021) in Matadi, Democratic Republic of the Congo.

Background: By the end of the third wave of the coronavirus disease 2019 (COVID-19) epidemic (May-October 2021), only 3130 of the 57 268 confirmed cases of coronavirus disease 2019 (COVID-19) in the Democratic Republic of the Congo (DRC) were reported in Kongo Central. This province, and especially its capital city, Matadi, has essential trade and exchanges with Kinshasa, the epicenter of the COVID-19 epidemic in DRC. Kinshasa accounted for 60.0% of all cases during the same period. The true burden of COVID-19 in Matadi is likely underestimated. In this study, we aimed to determine the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seroprevalence and associated risk factors after the third wave in Matadi. Methods: We conducted a population-based cross-sectional study in October 2021. Consenting participants were interviewed and tested using an enzyme-linked immunosorbent assay commercial kit. We applied univariable and multivariable analysis to evaluate factors associated with seropositivity and adjusted the seroprevalence for the test kit performance. Results: We included 2210 participants from 489 households. Female participants represented 59.1%. The median age was 27 years (interquartile range, 16-45 years). The crude SARS-CoV-2 seroprevalence was 82.3%. Age was identified as the main risk factor as younger age decreased the seropositivity odds. Accounting for clustering at the household level increased the seroprevalence to 83.2%. The seroprevalence increased further to 88.1% (95% confidence interval, 86.2%-90.1%) after correcting for the laboratory test kit performance. Conclusions: The SARS-CoV-2 seroprevalence was very high, contrasting with reported cases. Evidence generated from this population-based survey remains relevant in guiding the local COVID-19 response, especially vaccination strategies.